Fitting a structure with an unrecognized residue to an EM density

[Anonymous]

I’m using “rosetta_src_2017.36.59679_bundle”. I’m trying to run the following bash script:

#!/bin/bash



$ROSETTA3/source/bin/rosetta_scripts.linuxgccrelease 

-in::file: /home/labusr/Documents/tubulin_PF_dep_noligand.pdb

-parser::protocol /home/labusr/Documents/A_asymm_refine.xml 

-parser::script_vars denswt=35 rms=1.5 reso=4.3 map=/home/labusr/Documents/tublin_map_masked.mrc testmap=/home/labusr/Documents/tubulin_test_map_right.mrc

-ignore_unrecognized_res 

-edensity::mapreso 4.3 

-default_max_cycles 200 

-edensity::cryoem_scatterers 

-beta 

-out::suffix _$1 

-crystal_refine

 

Even though I’m using the flag -ignore_unrecognized_res, I’m getting this error here: 

BACKTRACE:

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7f7a7576948f]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::string const&, utility::vector1<std::shared_ptr<core::chemical::ResidueType const>, std::allocator<std::shared_ptr<core::chemical::ResidueType const> > > const&)+0x5b1) [0x7f7a785053c1]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::string const&)+0xe1) [0x7f7a7850e3a1]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types()+0x472) [0x7f7a7850f2a2]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(core::io::StructFileRep const&, core::pose::Pose&)+0x30) [0x7f7a78510720]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::build_pose_as_is(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xc3) [0x7f7a79c06383]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::build_pose(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xab) [0x7f7a79c0682b]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x552) [0x7f7a79c0b392]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x50) [0x7f7a79c0c330]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, bool, core::import_pose::FileType)+0x3b) [0x7f7a79c0c51b]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr<protocols::jd2::Job>)+0x3d5) [0x7f7a7a64dd75]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x6aa) [0x7f7a7a62805a]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xc1) [0x7f7a7a629f71]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x4a) [0x7f7a7a6016ba]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403408]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f7a7375ec05]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403d4b]

./Tublin_exercise_refine.sh: line 8: -in:ignore_unrecognized_res: command not found

core.init: Rosetta version rosetta.source.release-152:d6547f6858282e67c41356255dfdd63b0e7a75aa 2017-09-08 02:01:37.594540 from http://www.rosettacommons.org

core.init: command: /home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease -in::file: /home/labusr/Documents/tubulin_PF_dep_final.pdb -parser::protocol /home/labusr/Documents/A_asymm_refine.xml -parser::script_vars denswt=35 rms=1.5 reso=4.3 map=/home/labusr/Documents/tublin_map_masked.mrc testmap=/home/labusr/Documents/tubulin_test_map_right.mrc

core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1356985856 seed_offset=0 real_seed=1356985856

core.init.random: RandomGenerator:init: Normal mode, seed=1356985856 RG_type=mt19937

core.init: Resolved executable path: /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/rosetta_scripts.default.linuxgccrelease

core.init: Looking for database based on location of executable: /home/labusr/rosetta/main/database/

protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter

protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs

protocols.jd2.PDBJobInputter: pushed /home/labusr/Documents/tubulin_PF_dep_final.pdb nstruct index 1

protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... 

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: filling pose from PDB /home/labusr/Documents/tubulin_PF_dep_final.pdb

core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 557 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 0.61 seconds.

core.import_pose.import_pose: File '/home/labusr/Documents/tubulin_PF_dep_final.pdb' automatically determined to be of type PDB

Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'tubulin_PF_dep_final_0001'

Error: [ ERROR ] 



[ ERROR ] EXCN_utility_exit has been thrown from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 1217

ERROR: Unrecognized residue: GTP





Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: tubulin_PF_dep_final_0001

protocols.jd2.JobDistributor: no more batches to process... 

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 3 seconds

Error: [ ERROR ] Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages

Error: [ ERROR ] 



ERROR: Unrecognized residue: GTP

ERROR:: Exit from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 1217

BACKTRACE:

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7fd3c412b48f]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::string const&, utility::vector1<std::shared_ptr<core::chemical::ResidueType const>, std::allocator<std::shared_ptr<core::chemical::ResidueType const> > > const&)+0x5b1) [0x7fd3c6ec73c1]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(unsigned long, std::string const&)+0xe1) [0x7fd3c6ed03a1]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types()+0x472) [0x7fd3c6ed12a2]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(core::io::StructFileRep const&, core::pose::Pose&)+0x30) [0x7fd3c6ed2720]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::build_pose_as_is(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xc3) [0x7fd3c85c8383]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::build_pose(std::shared_ptr<core::io::StructFileRep>, core::pose::Pose&, core::chemical::ResidueTypeSet const&, core::import_pose::ImportPoseOptions const&)+0xab) [0x7fd3c85c882b]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x552) [0x7fd3c85cd392]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x50) [0x7fd3c85ce330]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, bool, core::import_pose::FileType)+0x3b) [0x7fd3c85ce51b]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr<protocols::jd2::Job>)+0x3d5) [0x7fd3c900fd75]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x6aa) [0x7fd3c8fea05a]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xc1) [0x7fd3c8febf71]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x4a) [0x7fd3c8fc36ba]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403408]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd3c2120c05]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403d4b]

./Tublin_exercise_refine.sh: line 8: -in:ignore_unrecognized_res: command not found

 

 

[Anonymous]

Each line needs to end with a in your bash script otherwise the flags after it won’t be read. Make sure the line that starts with -parser_script_vars is on the same line that has testmap=… and then put a “” at the end of the line. That should resolve the issue.

[Anonymous]

Thanks. It works now. I did try the script on the structure after removing the ligand. I got an error related to the density. You can find more details here: https://www.rosettacommons.org/node/10118. Cheers. 

[Author]

Posts